Home

Citation: HOU Ji-Xuan, SI Li-Ming. Optimization Theory for Neighbor List Al rithmin Fluid System Simulation[J]. Acta Physico-Chimica Sinica, ;2009, 25(03): 430-434. doi: 10.3866/PKU.WHXB20090306 shu

Optimization Theory for Neighbor List Al rithmin Fluid System Simulation

HOU Ji-Xuan ,
SI Li-Ming ^,

1.
Laboratoire de Physique, UMR 5182 CNRS, Ecole Normale Superieure de Lyon, 46, Allee d'Italie F-69364 Lyon Cedex 07, France; Department of Electronic Engineering, School of Information Science and Technology, Beijing Institute of Technology, Beijing 100081, P. R. China

Corresponding author: SI Li-Ming, siliming100@yahoo.com.cn
Received Date: 25 August 2008
Available Online: 10 December 2008

The efficiency of the neighbor list al rithm in molecular dynamics simulation depends on the parameters chosen. By using the free-particle approximation and the diffusion approximation we can calculate the central processing unit (CPU) time that is used for the simulation. The free-particle approximation can be used in the case of low density or a small skin radius while the diffusion approximation can be used in the case of high density or a large skin radius. Combining the results of these two approximations optimal parameters may be selected and thus CPU time can be saved. Our result coincides with the result of the simulation based on Lennard-Jones fluid systems.
- Computational techniques,
- Molecular dynamics calculation,
- Fluid system
1. [1]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
2. [2]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
3. [3]
  Shanghua Li , Malin Li , Xiwen Chi , Xin Yin , Zhaodi Luo , Jihong Yu . 基于高离子迁移动力学的取向ZnQ分子筛保护层实现高稳定水系锌金属负极的构筑. Acta Physico-Chimica Sinica, 2025, 41(1): 2309003-. doi: 10.3866/PKU.WHXB202309003
4. [4]
  Qian Peng , Pengfei Yao , Zicong Wang , Xiufang Xu , Hongwei Sun . Promote the Training of Top Talents by Optimizing the Theoretical Computational Chemistry Curriculum System. University Chemistry, 2025, 40(5): 261-267. doi: 10.12461/PKU.DXHX202408012
5. [5]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
6. [6]
  Jiayu Gu , Siqi Wang , Jun Ling . Kinetics of Living Copolymerization: A Brief Discussion. University Chemistry, 2025, 40(4): 100-107. doi: 10.12461/PKU.DXHX202406012
7. [7]
  Supin Zhao , Jing Xie . Understanding the Vibrational Stark Effect of Water Molecules Using Quantum Chemistry Calculations. University Chemistry, 2025, 40(3): 178-185. doi: 10.12461/PKU.DXHX202406024
8. [8]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
9. [9]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
10. [10]
  Wen-Bing Hu . Systematic Introduction of Polymer Chain Structures. University Chemistry, 2025, 40(4): 15-19. doi: 10.3866/PKU.DXHX202401014
11. [11]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
12. [12]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
13. [13]
  Jiying Liu , Zehua Li , Wenjing Zhang , Donghui Wei . Molecular Orbital and Nucleus-Independent Chemical Shift Calculations for C₆H₆ and B₁₂H₁₂^2-: A Computational Chemistry Experiment. University Chemistry, 2025, 40(3): 186-192. doi: 10.12461/PKU.DXHX202406085
14. [14]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
15. [15]
  Zhenming Xu , Yibo Wang , Zhenhui Liu , Duo Chen , Mingbo Zheng , Laifa Shen . Experimental Design of Computational Materials Science and Computational Chemistry Courses Based on the Bohrium Scientific Computing Cloud Platform. University Chemistry, 2025, 40(3): 36-41. doi: 10.12461/PKU.DXHX202403096
16. [16]
  Jia Zhou . Constructing Potential Energy Surface of Water Molecule by Quantum Chemistry and Machine Learning: Introduction to a Comprehensive Computational Chemistry Experiment. University Chemistry, 2024, 39(3): 351-358. doi: 10.3866/PKU.DXHX202309060
17. [17]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185
18. [18]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
19. [19]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . 基于激发态手性铜催化的烯烃E→Z异构的动力学拆分——推荐一个本科生综合化学实验. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
20. [20]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063

Get Citation

PDF

XML

Metrics

PDF Downloads(1557)
Abstract views(3471)
HTML views(13)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Address：Zhongguancun North First Street 2,100190 Beijing, PR China Tel: +86-010-82449177-888

DownLoad: Full-Size Img PowerPoint

Return